From a84946903ab260dca9210a132349da825e8ab9a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20Brand=C3=A3o?= <555migalves555@gmail.com> Date: Wed, 20 Sep 2023 10:54:06 +0100 Subject: [PATCH 1/4] skeleton for pr MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Miguel Brandão <555migalves555@gmail.com> --- examples/scanned_document_export/README.md | 24 ++ .../upload_and_explore_pdfs.ipynb | 396 ++++++++++++++++++ 2 files changed, 420 insertions(+) create mode 100644 examples/scanned_document_export/README.md create mode 100644 examples/scanned_document_export/upload_and_explore_pdfs.ipynb diff --git a/examples/scanned_document_export/README.md b/examples/scanned_document_export/README.md new file mode 100644 index 0000000..efb3b4e --- /dev/null +++ b/examples/scanned_document_export/README.md @@ -0,0 +1,24 @@ +# Bring Your Own PDFs + +In this example we expand upon [Bringing Your Own PDF](../bring_your_own_pdf) with more functionality. +We will create a new data index to which we will upload scanned pdf documents that will be OCRed, this will +allow you to explore their contents with the full capabilities of Deep Search. + + +## Access required + +The content of this notebook requires access to Deep Search capabilities which are not +available on the public access system. + +[Contact us](https://ds4sd.github.io/#unlimited-access) if you are interested in exploring +this Deep Search capabilities. + +### Authentication for the restricted instance + +When authenticating to Deep Search, you have to use the host of the restricted instance, for example + +```console +deepsearch login --host https://deepsearch-ext-v2-535206b87b82b5365d9d6671fbc19165-0000.us-south.containers.appdomain.cloud/ --output ../../ds-auth.ext-v2.json +``` + + diff --git a/examples/scanned_document_export/upload_and_explore_pdfs.ipynb b/examples/scanned_document_export/upload_and_explore_pdfs.ipynb new file mode 100644 index 0000000..2cbb70e --- /dev/null +++ b/examples/scanned_document_export/upload_and_explore_pdfs.ipynb @@ -0,0 +1,396 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "8ee29891", + "metadata": {}, + "source": [ + "# Bring Your Own PDFs\n", + "\n", + "In this example we combine the document conversion capabilities of Deep Search with its data query capabilities.\n", + "From the Deep Search Workspace, we create a new project data index which can host our own PDF documents.\n", + "Once the upload is completed, we will be able to query the documents, similar to the public data which we\n", + "explored in the [Data query quick start example](../data_query_quick_start/). \n", + "\n", + "\n", + "### Access required\n", + "\n", + "The content of this notebook requires access to Deep Search capabilities which are not\n", + "available on the public access system.\n", + "\n", + "[Contact us](https://ds4sd.github.io/#unlimited-access) if you are interested in exploring\n", + "this Deep Search capabilities." + ] + }, + { + "cell_type": "markdown", + "id": "d9727409", + "metadata": {}, + "source": [ + "### Authentication via stored credentials\n", + "\n", + "In this example, we initialize the Deep Search client from the credentials\n", + "contained in the file `../../ds-auth.ext-v2.json`. This can be generated with\n", + "\n", + "```shell\n", + "!deepsearch login --host https://deepsearch-ext-v2-535206b87b82b5365d9d6671fbc19165-0000.us-south.containers.appdomain.cloud/ --output ../../ds-auth.ext-v2.json\n", + "```\n", + "\n", + "The extra `--host` argument is required in this example to target the limited access instance\n", + "\n", + "More details in the [docs](https://ds4sd.github.io/deepsearch-toolkit/getting_started/#authentication)." + ] + }, + { + "cell_type": "markdown", + "id": "5d8e88b4", + "metadata": {}, + "source": [ + "### Notebooks parameters\n", + "\n", + "The following block defines the parameters used to execute the notebook\n", + "\n", + "- `CONFIG_FILE`: location of the Deep Search configuration file\n", + "- `PROJ_NAME`: the name for the project to create\n", + "- `INDEX_NAME`: the name for the data index to create\n", + "- `INPUT_FILES_FOLDER`: the files to upload\n", + "- `CLEANUP`: if true, it will delete the resources at the end of the execution" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "13560ae0", + "metadata": {}, + "outputs": [], + "source": [ + "# Input parameters for the example flow\n", + "from pathlib import Path\n", + "import datetime\n", + "CONFIG_FILE = Path(\"../../ds-auth.ext-v2.json\")\n", + "\n", + "timestamp = datetime.datetime.now()\n", + "PROJ_NAME = f\"Example project of {timestamp.strftime('%Y%m%d')}\"\n", + "INDEX_NAME = f\"Example docs upload {timestamp.strftime('%Y%m%d %H%M%S')}\"\n", + "INPUT_FILES_FOLDER = Path(\"../../data/samples/\")\n", + "\n", + "# Cleanup\n", + "CLEANUP = True" + ] + }, + { + "cell_type": "markdown", + "id": "0531c9c4", + "metadata": {}, + "source": [ + "### Import example dependencies" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "1ea3cd26", + "metadata": {}, + "outputs": [], + "source": [ + "# Import standard dependenices\n", + "import datetime\n", + "from copy import deepcopy\n", + "from tqdm.notebook import tqdm\n", + "import pandas as pd\n", + "\n", + "# IPython utilities\n", + "from IPython.display import display, Markdown, HTML, display_html\n", + "\n", + "# Import the deepsearch-toolkit\n", + "import deepsearch as ds\n", + "from deepsearch.cps.queries import DataQuery\n", + "from deepsearch.cps.client.components.queries import RunQueryError\n", + "from deepsearch.cps.data_indices import utils as data_indices_utils\n" + ] + }, + { + "cell_type": "markdown", + "id": "8f8be733", + "metadata": {}, + "source": [ + "### Connect to Deep Search" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "fae4dee3", + "metadata": {}, + "outputs": [], + "source": [ + "# Initialize the Deep Search client from the config file\n", + "config = ds.DeepSearchConfig.parse_file(CONFIG_FILE)\n", + "client = ds.CpsApiClient(config)\n", + "api = ds.CpsApi(client)" + ] + }, + { + "cell_type": "markdown", + "id": "18957147", + "metadata": {}, + "source": [ + "### Create data index and upload data" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "f5496626", + "metadata": {}, + "outputs": [], + "source": [ + "# Create example project\n", + "proj = api.projects.create(name=PROJ_NAME)\n", + "# Create a new data index in your project\n", + "data_index = api.data_indices.create(proj_key=proj.key, name=INDEX_NAME)" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "530fd67a", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Completed successfully\n" + ] + } + ], + "source": [ + "# Upload and convert documents\n", + "data_indices_utils.upload_files(api=api, coords=data_index.source, local_file=INPUT_FILES_FOLDER)" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "bfe83b90", + "metadata": {}, + "outputs": [ + { + "data": { + "text/markdown": [ + "The data is now available. You can query it programmatically (see next section) or access it via the Deep Search UI at
https://deepsearch-ext-v2-535206b87b82b5365d9d6671fbc19165-0000.us-south.containers.appdomain.cloud//projects/67a639f5db9c17b928c8c132b57a9be4a8eac33c/data/project/2b686a64ffd68efe39f30b1e25be9c71da437129/" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "display(Markdown(f\"The data is now available. You can query it programmatically (see next section) or access it via the Deep Search UI at
{api.client.config.host}/projects/{data_index.source.proj_key}/data/project/{data_index.source.index_key}/\"))\n" + ] + }, + { + "cell_type": "markdown", + "id": "45ec4a93", + "metadata": {}, + "source": [ + "### Query your data" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "6a9a31ab", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "The data index contains 2 entries.\n" + ] + } + ], + "source": [ + "# Count the documents in the data index\n", + "query = DataQuery(\"*\", source=[\"\"], limit=0, coordinates=data_index.source)\n", + "query_results = api.queries.run(query)\n", + "print(f\"The data index contains {query_results.outputs['data_count']} entries.\")" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "a669e5a9", + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "ca9ff7c152b6495d8e18e833a9047039", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "0it [00:00, ?it/s]" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "Finished fetching all data. Total is 1 records.\n" + ] + } + ], + "source": [ + "# Find documents matching query\n", + "search_query = \"speedup\"\n", + "query = DataQuery(search_query, source=[\"description.title\", \"description.authors\"], coordinates=data_index.source)\n", + "query_results = api.queries.run(query)\n", + "\n", + "all_results = []\n", + "cursor = api.queries.run_paginated_query(query)\n", + "for result_page in tqdm(cursor):\n", + " # Iterate through the results of a single page, and add to the total list\n", + " for row in result_page.outputs[\"data_outputs\"]: \n", + " print()\n", + " # Add row to results table\n", + " all_results.append({\n", + " \"Title\": row[\"_source\"][\"description\"][\"title\"],\n", + " \"Authors\": \", \".join([author[\"name\"] for author in row[\"_source\"][\"description\"].get(\"authors\", [])]),\n", + " }) \n", + "\n", + "print(f'Finished fetching all data. Total is {len(all_results)} records.')" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "e997bbae", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
TitleAuthors
0Delivering Document Conversion as a Cloud Service with High Throughput and Responsiveness
" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# Visualize the table with all results\n", + "df = pd.json_normalize(all_results)\n", + "display(HTML(df.head().to_html(render_links=True)))" + ] + }, + { + "cell_type": "markdown", + "id": "b13b5f9e", + "metadata": {}, + "source": [ + "### Cleanup\n", + "If enabled, we will delete all the resources created in the example" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "9a0b82b8", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Project data deleted\n" + ] + } + ], + "source": [ + "# Delete data index\n", + "if CLEANUP:\n", + " api.data_indices.delete(data_index.source)\n", + " print(\"Project data deleted\")" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "bb1aec5c", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Project deleted\n" + ] + } + ], + "source": [ + "# Delete project\n", + "if CLEANUP:\n", + " api.projects.remove(project=proj)\n", + " print(\"Project deleted\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1a611b03", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.8" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From 9de89ba1c271cf2ff3d7afb330fa54d2b500832b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20Brand=C3=A3o?= <555migalves555@gmail.com> Date: Mon, 2 Oct 2023 11:41:06 +0100 Subject: [PATCH 2/4] working OCR example MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Miguel Brandão <555migalves555@gmail.com> --- .../upload_and_explore_pdfs.ipynb | 36 +- poetry.lock | 2738 +++++++++-------- pyproject.toml | 2 +- 3 files changed, 1450 insertions(+), 1326 deletions(-) diff --git a/examples/scanned_document_export/upload_and_explore_pdfs.ipynb b/examples/scanned_document_export/upload_and_explore_pdfs.ipynb index 2cbb70e..ad74999 100644 --- a/examples/scanned_document_export/upload_and_explore_pdfs.ipynb +++ b/examples/scanned_document_export/upload_and_explore_pdfs.ipynb @@ -59,7 +59,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 9, "id": "13560ae0", "metadata": {}, "outputs": [], @@ -72,7 +72,7 @@ "timestamp = datetime.datetime.now()\n", "PROJ_NAME = f\"Example project of {timestamp.strftime('%Y%m%d')}\"\n", "INDEX_NAME = f\"Example docs upload {timestamp.strftime('%Y%m%d %H%M%S')}\"\n", - "INPUT_FILES_FOLDER = Path(\"../../data/samples/\")\n", + "INPUT_FILES_FOLDER = Path(\"../../data/samples/scanned_documents\")\n", "\n", "# Cleanup\n", "CLEANUP = True" @@ -88,7 +88,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 10, "id": "1ea3cd26", "metadata": {}, "outputs": [], @@ -106,7 +106,8 @@ "import deepsearch as ds\n", "from deepsearch.cps.queries import DataQuery\n", "from deepsearch.cps.client.components.queries import RunQueryError\n", - "from deepsearch.cps.data_indices import utils as data_indices_utils\n" + "from deepsearch.cps.data_indices import utils as data_indices_utils\n", + "from deepsearch.documents.core.models import ConversionSettings\n" ] }, { @@ -119,7 +120,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 11, "id": "fae4dee3", "metadata": {}, "outputs": [], @@ -140,7 +141,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 12, "id": "f5496626", "metadata": {}, "outputs": [], @@ -153,21 +154,20 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 13, "id": "530fd67a", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Completed successfully\n" - ] - } - ], + "outputs": [], "source": [ "# Upload and convert documents\n", - "data_indices_utils.upload_files(api=api, coords=data_index.source, local_file=INPUT_FILES_FOLDER)" + "#Define the OCR to be used\n", + "conv_settings = ConversionSettings().from_project(api, proj_key=proj.key)\n", + "conv_settings.ocr.enabled= True\n", + "conv_settings.ocr.merge_mode= 'prioritize-ocr'\n", + "conv_settings.ocr.backend= 'alpine-ocr'\n", + "\n", + "\n", + "data_indices_utils.upload_files(api=api, coords=data_index.source, local_file=INPUT_FILES_FOLDER, conv_settings=conv_settings)" ] }, { @@ -388,7 +388,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.8" + "version": "3.9.16" } }, "nbformat": 4, diff --git a/poetry.lock b/poetry.lock index b531ca7..f840fc5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,32 +1,30 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. [[package]] name = "anyio" -version = "3.7.1" +version = "4.0.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" -category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "anyio-3.7.1-py3-none-any.whl", hash = "sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5"}, - {file = "anyio-3.7.1.tar.gz", hash = "sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780"}, + {file = "anyio-4.0.0-py3-none-any.whl", hash = "sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f"}, + {file = "anyio-4.0.0.tar.gz", hash = "sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a"}, ] [package.dependencies] -exceptiongroup = {version = "*", markers = "python_version < \"3.11\""} +exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" [package.extras] -doc = ["Sphinx", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.2.2)", "sphinxcontrib-jquery"] -test = ["anyio[trio]", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] -trio = ["trio (<0.22)"] +doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +trio = ["trio (>=0.22)"] [[package]] name = "appnope" version = "0.1.3" description = "Disable App Nap on macOS >= 10.9" -category = "main" optional = false python-versions = "*" files = [ @@ -38,7 +36,6 @@ files = [ name = "argilla" version = "1.11.0" description = "Open-source tool for exploring, labeling, and monitoring data for NLP projects." -category = "main" optional = false python-versions = "<3.12,>=3.8" files = [ @@ -69,29 +66,28 @@ tests = ["factory-boy (>=3.2.1,<3.3.0)", "pytest", "pytest-asyncio", "pytest-cov [[package]] name = "argon2-cffi" -version = "21.3.0" -description = "The secure Argon2 password hashing algorithm." -category = "main" +version = "23.1.0" +description = "Argon2 for Python" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "argon2-cffi-21.3.0.tar.gz", hash = "sha256:d384164d944190a7dd7ef22c6aa3ff197da12962bd04b17f64d4e93d934dba5b"}, - {file = "argon2_cffi-21.3.0-py3-none-any.whl", hash = "sha256:8c976986f2c5c0e5000919e6de187906cfd81fb1c72bf9d88c01177e77da7f80"}, + {file = "argon2_cffi-23.1.0-py3-none-any.whl", hash = "sha256:c670642b78ba29641818ab2e68bd4e6a78ba53b7eff7b4c3815ae16abf91c7ea"}, + {file = "argon2_cffi-23.1.0.tar.gz", hash = "sha256:879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08"}, ] [package.dependencies] argon2-cffi-bindings = "*" [package.extras] -dev = ["cogapp", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "pre-commit", "pytest", "sphinx", "sphinx-notfound-page", "tomli"] -docs = ["furo", "sphinx", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest"] +dev = ["argon2-cffi[tests,typing]", "tox (>4)"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-copybutton", "sphinx-notfound-page"] +tests = ["hypothesis", "pytest"] +typing = ["mypy"] [[package]] name = "argon2-cffi-bindings" version = "21.2.0" description = "Low-level CFFI bindings for Argon2" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -127,42 +123,58 @@ tests = ["pytest"] [[package]] name = "arrow" -version = "1.2.3" +version = "1.3.0" description = "Better dates & times for Python" -category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.8" files = [ - {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, - {file = "arrow-1.2.3.tar.gz", hash = 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{file = "zipp-3.16.0-py3-none-any.whl", hash = "sha256:5dadc3ad0a1f825fe42ce1bce0f2fc5a13af2e6b2d386af5b0ff295bc0a287d3"}, - {file = "zipp-3.16.0.tar.gz", hash = "sha256:1876cb065531855bbe83b6c489dcf69ecc28f1068d8e95959fe8bbc77774c941"}, + {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, + {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [metadata] lock-version = "2.0" python-versions = ">= 3.8, <3.11" -content-hash = "0628372703225eb95da11298afff9cb231697bd8b3cfb60c5fcc6929e5188283" +content-hash = "afe40dc3ae15e6900ceaaa4c86a0e80b6e7ea90af87258dc84b76e5213ff761b" diff --git a/pyproject.toml b/pyproject.toml index a871a83..1f234e6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,7 @@ packages = [] [tool.poetry.dependencies] python = ">= 3.8, <3.11" -deepsearch-toolkit = "^0.19.1" +deepsearch-toolkit = "^0.28.0" jupyter = "^1.0.0" ipywidgets = "^7" # previous major release is needed bcause of mols2grid numpy = "^1.23.4" From eccf8d81e412dcb9116ca41f03f3f41fbaf48a21 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20Brand=C3=A3o?= <555migalves555@gmail.com> Date: Mon, 2 Oct 2023 11:49:23 +0100 Subject: [PATCH 3/4] updated access required README section MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Miguel Brandão <555migalves555@gmail.com> --- examples/scanned_document_export/README.md | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/examples/scanned_document_export/README.md b/examples/scanned_document_export/README.md index efb3b4e..f414da0 100644 --- a/examples/scanned_document_export/README.md +++ b/examples/scanned_document_export/README.md @@ -5,20 +5,11 @@ We will create a new data index to which we will upload scanned pdf documents th allow you to explore their contents with the full capabilities of Deep Search. -## Access required +### Access required The content of this notebook requires access to Deep Search capabilities which are not available on the public access system. -[Contact us](https://ds4sd.github.io/#unlimited-access) if you are interested in exploring -this Deep Search capabilities. - -### Authentication for the restricted instance - -When authenticating to Deep Search, you have to use the host of the restricted instance, for example - -```console -deepsearch login --host https://deepsearch-ext-v2-535206b87b82b5365d9d6671fbc19165-0000.us-south.containers.appdomain.cloud/ --output ../../ds-auth.ext-v2.json -``` - +[Contact us](https://ds4sd.github.io/) if you are interested in exploring +the enterprise-level Deep Search capabilities. From 93e66fcaf4c87b7e0903b2d95a1085f5e601ace1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20Brand=C3=A3o?= <555migalves555@gmail.com> Date: Mon, 2 Oct 2023 12:14:21 +0100 Subject: [PATCH 4/4] Separated samples to regular and scanned pdfs, some updates to scanned document visualization notebook MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Miguel Brandão <555migalves555@gmail.com> --- data/samples/{ => pdf_samples}/2206.00785.pdf | Bin data/samples/{ => pdf_samples}/2206.01062.pdf | Bin .../upload_and_explore_pdfs.ipynb | 4 +- .../README.md | 0 .../upload_and_explore_pdfs.ipynb | 122 ++++++++++-------- 5 files changed, 68 insertions(+), 58 deletions(-) rename data/samples/{ => pdf_samples}/2206.00785.pdf (100%) rename data/samples/{ => pdf_samples}/2206.01062.pdf (100%) rename examples/{scanned_document_export => bring_your_own_scanned_pdf}/README.md (100%) rename examples/{scanned_document_export => bring_your_own_scanned_pdf}/upload_and_explore_pdfs.ipynb (77%) diff --git a/data/samples/2206.00785.pdf b/data/samples/pdf_samples/2206.00785.pdf similarity index 100% rename from data/samples/2206.00785.pdf rename to data/samples/pdf_samples/2206.00785.pdf diff --git a/data/samples/2206.01062.pdf b/data/samples/pdf_samples/2206.01062.pdf similarity index 100% rename from data/samples/2206.01062.pdf rename to data/samples/pdf_samples/2206.01062.pdf diff --git a/examples/bring_your_own_pdf/upload_and_explore_pdfs.ipynb b/examples/bring_your_own_pdf/upload_and_explore_pdfs.ipynb index 2cbb70e..eaa617b 100644 --- a/examples/bring_your_own_pdf/upload_and_explore_pdfs.ipynb +++ b/examples/bring_your_own_pdf/upload_and_explore_pdfs.ipynb @@ -72,7 +72,7 @@ "timestamp = datetime.datetime.now()\n", "PROJ_NAME = f\"Example project of {timestamp.strftime('%Y%m%d')}\"\n", "INDEX_NAME = f\"Example docs upload {timestamp.strftime('%Y%m%d %H%M%S')}\"\n", - "INPUT_FILES_FOLDER = Path(\"../../data/samples/\")\n", + "INPUT_FILES_FOLDER = Path(\"../../data/samples/pdf_samples\")\n", "\n", "# Cleanup\n", "CLEANUP = True" @@ -388,7 +388,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.8" + "version": "3.9.16" } }, "nbformat": 4, diff --git a/examples/scanned_document_export/README.md b/examples/bring_your_own_scanned_pdf/README.md similarity index 100% rename from examples/scanned_document_export/README.md rename to examples/bring_your_own_scanned_pdf/README.md diff --git a/examples/scanned_document_export/upload_and_explore_pdfs.ipynb b/examples/bring_your_own_scanned_pdf/upload_and_explore_pdfs.ipynb similarity index 77% rename from examples/scanned_document_export/upload_and_explore_pdfs.ipynb rename to examples/bring_your_own_scanned_pdf/upload_and_explore_pdfs.ipynb index ad74999..0f7de2d 100644 --- a/examples/scanned_document_export/upload_and_explore_pdfs.ipynb +++ b/examples/bring_your_own_scanned_pdf/upload_and_explore_pdfs.ipynb @@ -59,7 +59,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 18, "id": "13560ae0", "metadata": {}, "outputs": [], @@ -88,7 +88,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 19, "id": "1ea3cd26", "metadata": {}, "outputs": [], @@ -98,6 +98,8 @@ "from copy import deepcopy\n", "from tqdm.notebook import tqdm\n", "import pandas as pd\n", + "import tempfile\n", + "import json\n", "\n", "# IPython utilities\n", "from IPython.display import display, Markdown, HTML, display_html\n", @@ -120,7 +122,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 20, "id": "fae4dee3", "metadata": {}, "outputs": [], @@ -141,7 +143,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 28, "id": "f5496626", "metadata": {}, "outputs": [], @@ -154,7 +156,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 29, "id": "530fd67a", "metadata": {}, "outputs": [], @@ -172,14 +174,14 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 30, "id": "bfe83b90", "metadata": {}, "outputs": [ { "data": { "text/markdown": [ - "The data is now available. You can query it programmatically (see next section) or access it via the Deep Search UI at
https://deepsearch-ext-v2-535206b87b82b5365d9d6671fbc19165-0000.us-south.containers.appdomain.cloud//projects/67a639f5db9c17b928c8c132b57a9be4a8eac33c/data/project/2b686a64ffd68efe39f30b1e25be9c71da437129/" + "The data is now available. You can query it programmatically (see next section) or access it via the Deep Search UI at
https://cps.foc-deepsearch.zurich.ibm.com/projects/e6cd444006224102f0758e6666c09c8969dc94ab/data/project/8244be0d8f4e5e02e2c8db3ecab85a5bb5c418a7/" ], "text/plain": [ "" @@ -198,40 +200,19 @@ "id": "45ec4a93", "metadata": {}, "source": [ - "### Query your data" + "### Download your data" ] }, { "cell_type": "code", - "execution_count": 7, - "id": "6a9a31ab", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "The data index contains 2 entries.\n" - ] - } - ], - "source": [ - "# Count the documents in the data index\n", - "query = DataQuery(\"*\", source=[\"\"], limit=0, coordinates=data_index.source)\n", - "query_results = api.queries.run(query)\n", - "print(f\"The data index contains {query_results.outputs['data_count']} entries.\")" - ] - }, - { - "cell_type": "code", - "execution_count": 8, + "execution_count": 31, "id": "a669e5a9", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "ca9ff7c152b6495d8e18e833a9047039", + "model_id": "c5793cb814dd450eab77421f8f04eefe", "version_major": 2, "version_minor": 0 }, @@ -246,60 +227,89 @@ "name": "stdout", "output_type": "stream", "text": [ - "\n", - "Finished fetching all data. Total is 1 records.\n" + "'title'\n", + "Finished fetching all data. Total is 1 records.\n", + "Data downloaded in /tmp/tmpt_7juiy8\n" ] } ], "source": [ - "# Find documents matching query\n", - "search_query = \"speedup\"\n", - "query = DataQuery(search_query, source=[\"description.title\", \"description.authors\"], coordinates=data_index.source)\n", - "query_results = api.queries.run(query)\n", + "# Run query\n", + "query = DataQuery(search_query=\"*\", source=[\"*\"], coordinates=data_index.source)\n", + "cursor = api.queries.run_paginated_query(query)\n", + "\n", + "# Using a temp dir for demo purposes; to persist instead, set output dir accordingly\n", + "temp_dir = tempfile.TemporaryDirectory()\n", + "output_dir = temp_dir.name\n", "\n", + "# Iterate through query results\n", "all_results = []\n", - "cursor = api.queries.run_paginated_query(query)\n", "for result_page in tqdm(cursor):\n", - " # Iterate through the results of a single page, and add to the total list\n", - " for row in result_page.outputs[\"data_outputs\"]: \n", - " print()\n", - " # Add row to results table\n", - " all_results.append({\n", - " \"Title\": row[\"_source\"][\"description\"][\"title\"],\n", - " \"Authors\": \", \".join([author[\"name\"] for author in row[\"_source\"][\"description\"].get(\"authors\", [])]),\n", - " }) \n", + " for row in result_page.outputs[\"data_outputs\"]:\n", + "\n", + " # Download JSON file\n", + " file_path = Path(output_dir) / f\"{row['_id']}.json\"\n", + " with open(file_path, \"w\") as outfile:\n", + " json.dump(row[\"_source\"], outfile, indent=2)\n", + " try:\n", + " all_results.append({\n", + " \"Title\": row[\"_source\"][\"description\"][\"title\"],\n", + " \"Path\": file_path,\n", + " })\n", + " except KeyError as e:\n", + " print(e)\n", "\n", - "print(f'Finished fetching all data. Total is {len(all_results)} records.')" + "print(f\"Finished fetching all data. Total is {len(all_results)} records.\")\n", + "print(f\"Data downloaded in {output_dir}\")" ] }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 32, "id": "e997bbae", "metadata": {}, "outputs": [ { "data": { "text/html": [ + "
\n", + "\n", "\n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", - "
TitleAuthorsPath
0Delivering Document Conversion as a Cloud Service with High Throughput and ResponsivenessMissouri Public Water Systems BILL TO:/tmp/tmpt_7juiy8/780668c60178a66e31394f81ad092...
" + "\n", + "
" ], "text/plain": [ - "" + " Title \\\n", + "0 Missouri Public Water Systems BILL TO: \n", + "\n", + " Path \n", + "0 /tmp/tmpt_7juiy8/780668c60178a66e31394f81ad092... " ] }, "metadata": {}, @@ -309,7 +319,7 @@ "source": [ "# Visualize the table with all results\n", "df = pd.json_normalize(all_results)\n", - "display(HTML(df.head().to_html(render_links=True)))" + "display(df)" ] }, { @@ -323,7 +333,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 26, "id": "9a0b82b8", "metadata": {}, "outputs": [ @@ -344,7 +354,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 27, "id": "bb1aec5c", "metadata": {}, "outputs": [